PGAP4

post-GPI attachment to proteins GalNAc transferase 4

Basic information

Region (hg38): 9:101473170-101533537

Previous symbols: [ "C9orf125", "TMEM246" ]

Links

ENSG00000165152 ∙ NCBI:84302 ∙ OMIM:620264 ∙ HGNC:28180 ∙ Uniprot:Q9BRR3 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the PGAP4 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the PGAP4 gene is commonly pathogenic or not.

In the table, we include only reliable ClinVar variants with their consequences to MANE Select, Mane Plus Clinical transcripts, or transcripts with TSL equals 1. Click the count to view the source variants.

Warning: slight differences between displayed counts and the number of variants in ClinVar may occur, primarily due to (1) the application of a different transcript and/or consequence by our variant effect predictor or (2) differences in clinical significance: we classify Benign/Likely benign variants as Likely benign and Pathogenic/Likely pathogenic variants as Likely pathogenic.

Variant type	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous						0
missense			18			18
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	18	0	0

Variants in PGAP4

This is a list of pathogenic ClinVar variants found in the PGAP4 region.

You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.

Position	Type	Phenotype	Significance	ClinVar
9-101475910-G-A		not specified	Uncertain significance (Sep 17, 2021)
9-101475940-C-A		not specified	Uncertain significance (Dec 28, 2023)
9-101476033-C-G		not specified	Uncertain significance (Sep 14, 2023)
9-101476065-G-A		not specified	Uncertain significance (Feb 01, 2023)
9-101476144-G-A		not specified	Uncertain significance (Feb 08, 2023)
9-101476311-C-T		not specified	Uncertain significance (Sep 22, 2022)
9-101476407-C-T		not specified	Uncertain significance (Dec 11, 2023)
9-101476573-C-A		not specified	Uncertain significance (Aug 09, 2021)
9-101476609-C-T		not specified	Uncertain significance (Apr 01, 2024)
9-101476627-T-G		not specified	Uncertain significance (Feb 14, 2023)
9-101476723-G-T		not specified	Uncertain significance (Jan 08, 2024)
9-101476746-T-C		not specified	Uncertain significance (Jul 12, 2023)
9-101476774-T-C		not specified	Uncertain significance (Oct 06, 2021)
9-101476794-G-A		not specified	Uncertain significance (Oct 03, 2022)
9-101476846-G-A		not specified	Uncertain significance (Apr 09, 2024)
9-101476932-C-T		not specified	Uncertain significance (Nov 30, 2022)
9-101476959-C-T		not specified	Uncertain significance (Feb 01, 2023)
9-101477055-C-T		not specified	Uncertain significance (Apr 26, 2023)
9-101477056-G-C		not specified	Uncertain significance (Jul 25, 2023)
9-101477080-T-C		not specified	Uncertain significance (Mar 07, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
PGAP4	protein_coding	protein_coding	ENST00000374851	1	60367

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0939	0.899	125736	0	12	125748	0.0000477

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.42	177	239	0.742	0.0000145	2603
Missense in Polyphen		50	79.501	0.62892		887
Synonymous	-0.312	104	100	1.04	0.00000561	857
Loss of Function	2.34	4	13.1	0.304	7.37e-7	139

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000239	0.000239
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000544	0.0000544
Finnish	0.0000462	0.0000462
European (Non-Finnish)	0.0000265	0.0000264
Middle Eastern	0.0000544	0.0000544
South Asian	0.0000327	0.0000327
Other	0.00	0.00

dbNSFP

Source: dbNSFP

Intolerance Scores

• rvis_EVS: -0.36
• rvis_percentile_EVS: 29.16

Haploinsufficiency Scores

• pHI: 0.146
• hipred: Y
• hipred_score: 0.568
• ghis: 0.577

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	Medium	Medium	Medium
Primary Immunodeficiency	Medium	Medium	Medium
Cancer	Medium	Medium	Medium

Mouse Genome Informatics

• Gene name: Tmem246

Gene ontology

• Cellular component: integral component of membrane